Job request: 17035

version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_ethnicity_01GXRGGBFB9PNT42F46VMJGHRA:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity
      --param end_date="2023-04-05"
      --output-dir output/01GXRGGBFB9PNT42F46VMJGHRA --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GXRGGBFB9PNT42F46VMJGHRA/input_ethnicity.csv.gz


  generate_study_population_01GXRGGBFB9PNT42F46VMJGHRA:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="interactive_codelists/codelist_1.csv"
      --param codelist_1_type="medication"
      --param codelist_2_path="interactive_codelists/codelist_2.csv"
      --param codelist_2_type="event"
      --param codelist_1_frequency="monthly"
      --param time_value="4"
      --param time_scale="weeks"
      --param time_event="before"
      --param codelist_2_comparison_date="end_date"
      --param operator="AND"
      --param population="adults"
      --param breakdowns="sex,age,ethnicity,imd,region"
      --index-date-range="2019-09-01 to 2023-04-05 by month"
      --output-dir=output/01GXRGGBFB9PNT42F46VMJGHRA
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GXRGGBFB9PNT42F46VMJGHRA/input_*.csv.gz

  join_cohorts_01GXRGGBFB9PNT42F46VMJGHRA:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GXRGGBFB9PNT42F46VMJGHRA/input_20*.csv.gz
        --rhs output/01GXRGGBFB9PNT42F46VMJGHRA/input_ethnicity.csv.gz
        --output-dir output/01GXRGGBFB9PNT42F46VMJGHRA/joined
    needs: [generate_study_population_01GXRGGBFB9PNT42F46VMJGHRA, generate_study_population_ethnicity_01GXRGGBFB9PNT42F46VMJGHRA]
    outputs:
      highly_sensitive:
        cohort: output/01GXRGGBFB9PNT42F46VMJGHRA/joined/input_20*.csv.gz

  generate_measures_01GXRGGBFB9PNT42F46VMJGHRA:
    run: >
      python:latest -m analysis.measures
        --breakdowns="sex,age,ethnicity,imd,region"
        --input_dir="output/01GXRGGBFB9PNT42F46VMJGHRA/joined"
        --measure="med_review"

    needs: [join_cohorts_01GXRGGBFB9PNT42F46VMJGHRA]
    outputs:
      moderately_sensitive:
        measure: output/01GXRGGBFB9PNT42F46VMJGHRA/joined/measure*rate.csv
        decile_measure: output/01GXRGGBFB9PNT42F46VMJGHRA/joined/measure*rate_deciles.csv

  top_5_table_01GXRGGBFB9PNT42F46VMJGHRA:
    run: >
      python:latest python analysis/top_5.py
      --codelist-1-path="interactive_codelists/codelist_1.csv"
      --codelist-2-path="interactive_codelists/codelist_2.csv"
      --output-dir="output/01GXRGGBFB9PNT42F46VMJGHRA"
    needs: [generate_measures_01GXRGGBFB9PNT42F46VMJGHRA]
    outputs:
      moderately_sensitive:
        tables: output/01GXRGGBFB9PNT42F46VMJGHRA/joined/top_5*.csv

  deciles_chart_01GXRGGBFB9PNT42F46VMJGHRA:
    run: >
      deciles-charts:v0.0.33
        --input-files output/01GXRGGBFB9PNT42F46VMJGHRA/joined/measure_practice_rate_deciles.csv
        --output-dir output/01GXRGGBFB9PNT42F46VMJGHRA/joined
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_01GXRGGBFB9PNT42F46VMJGHRA]
    outputs:
      moderately_sensitive:
        deciles_charts: output/01GXRGGBFB9PNT42F46VMJGHRA/joined/deciles_*.*

  plot_measure_01GXRGGBFB9PNT42F46VMJGHRA:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns="sex,age,ethnicity,imd,region"
        --output-dir output/01GXRGGBFB9PNT42F46VMJGHRA
    needs: [generate_measures_01GXRGGBFB9PNT42F46VMJGHRA]
    outputs:
      moderately_sensitive:
        measure: output/01GXRGGBFB9PNT42F46VMJGHRA/plot_measure*.png

  event_counts_01GXRGGBFB9PNT42F46VMJGHRA:
    run: >
      python:latest python analysis/event_counts.py --input_dir="output/01GXRGGBFB9PNT42F46VMJGHRA/joined" --output_dir="output/01GXRGGBFB9PNT42F46VMJGHRA"
    needs: [join_cohorts_01GXRGGBFB9PNT42F46VMJGHRA]
    outputs:
      moderately_sensitive:
        measure: output/01GXRGGBFB9PNT42F46VMJGHRA/event_counts.json

  generate_report_01GXRGGBFB9PNT42F46VMJGHRA:
    run: >
      python:latest python analysis/render_report.py
      --output-dir="output/01GXRGGBFB9PNT42F46VMJGHRA"
      --report-title="Doxycycline (tetracyclines) & Chronic obstructive pulmonary disease (COPD) codes"
      --population="adults"
      --breakdowns="sex,age,ethnicity,imd,region"
      --codelist-1-name="Doxycycline (tetracyclines)"
      --codelist-2-name="Chronic obstructive pulmonary disease (COPD) codes"
      --codelist-1-link="user/alexorlek/doxycycline-tetracyclines/4458c45a"
      --codelist-2-link="nhsd-primary-care-domain-refsets/copd_cod/20210127"
      --time-value="4"
      --time-scale="weeks"
      --time-event="before"
      --start-date="2019-09-01"
      --end-date="2023-04-05"
    needs: [event_counts_01GXRGGBFB9PNT42F46VMJGHRA, deciles_chart_01GXRGGBFB9PNT42F46VMJGHRA, top_5_table_01GXRGGBFB9PNT42F46VMJGHRA, plot_measure_01GXRGGBFB9PNT42F46VMJGHRA]
    outputs:
      moderately_sensitive:
        notebook: output/01GXRGGBFB9PNT42F46VMJGHRA/report.html